Repackage

Author: Mark Robinson

src/main/java/org/commonwl/viewer/domain/Workflow.java

@@ -19,6 +19,8 @@
 
 package org.commonwl.viewer.domain;
 
+import org.commonwl.viewer.domain.cwl.CWLElement;
+import org.commonwl.viewer.domain.cwl.CWLStep;
 import org.commonwl.viewer.services.DotWriter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

…ommonwl/viewer/domain/CWLCollection.java …nwl/viewer/domain/cwl/CWLCollection.javasrc/main/java/org/commonwl/viewer/domain/CWLCollection.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/CWLCollection.java src/main/java/org/commonwl/viewer/domain/CWLCollection.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/CWLCollection.java

@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain;
+package org.commonwl.viewer.domain.cwl;
 
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -26,9 +26,10 @@
 import com.fasterxml.jackson.databind.node.TextNode;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
+import org.commonwl.viewer.domain.GithubDetails;
+import org.commonwl.viewer.domain.Workflow;
 import org.commonwl.viewer.services.DockerService;
 import org.commonwl.viewer.services.GitHubService;
-import org.commonwl.viewer.web.PathTraversalException;
 import org.eclipse.egit.github.core.RepositoryContents;
 import org.yaml.snakeyaml.Yaml;
 
@@ -298,7 +299,7 @@ private void fillStepRunTypes(Workflow workflow) throws PathTraversalException {
                     runDoc = cwlDocs.get(runParam.substring(1));
                 } else {
                     Path basePath = Paths.get(githubInfo.getPath());
-                    Path filePath = basePath.resolve(runParam);
+                    Path filePath = basePath.resolve(runParam).normalize();
                     if (!filePath.startsWith(basePath)) {
                         throw new PathTraversalException("Step run parameter path '" + filePath +
                                 "' is outside base path '" + basePath + "'");

…g/commonwl/viewer/domain/CWLElement.java …mmonwl/viewer/domain/cwl/CWLElement.javasrc/main/java/org/commonwl/viewer/domain/CWLElement.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/CWLElement.java src/main/java/org/commonwl/viewer/domain/CWLElement.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/CWLElement.java

@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain;
+package org.commonwl.viewer.domain.cwl;
 
 import java.util.ArrayList;
 import java.util.List;

…g/commonwl/viewer/domain/CWLProcess.java …mmonwl/viewer/domain/cwl/CWLProcess.javasrc/main/java/org/commonwl/viewer/domain/CWLProcess.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/CWLProcess.java src/main/java/org/commonwl/viewer/domain/CWLProcess.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/CWLProcess.java

@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain;
+package org.commonwl.viewer.domain.cwl;
 
 /**
  * Enum for possible CWL processes

…/org/commonwl/viewer/domain/CWLStep.java …/commonwl/viewer/domain/cwl/CWLStep.javasrc/main/java/org/commonwl/viewer/domain/CWLStep.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/CWLStep.java src/main/java/org/commonwl/viewer/domain/CWLStep.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/CWLStep.java

@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain;
+package org.commonwl.viewer.domain.cwl;
 
 import java.util.Map;
 

…l/viewer/web/PathTraversalException.java …r/domain/cwl/PathTraversalException.javasrc/main/java/org/commonwl/viewer/web/PathTraversalException.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/PathTraversalException.java src/main/java/org/commonwl/viewer/web/PathTraversalException.java renamed to src/main/java/org/commonwl/viewer/domain/cwl/PathTraversalException.java

@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.web;
+package org.commonwl.viewer.domain.cwl;
 
 /**
  * Exception thrown when a potential path traversal attempt was prevented

…ommonwl/viewer/domain/HashableAgent.java …domain/researchobject/HashableAgent.javasrc/main/java/org/commonwl/viewer/domain/HashableAgent.java renamed to src/main/java/org/commonwl/viewer/domain/researchobject/HashableAgent.java src/main/java/org/commonwl/viewer/domain/HashableAgent.java renamed to src/main/java/org/commonwl/viewer/domain/researchobject/HashableAgent.java

@@ -1,4 +1,4 @@
-package org.commonwl.viewer.domain;
+package org.commonwl.viewer.domain.researchobject;
 
 import org.apache.taverna.robundle.manifest.Agent;
 

…org/commonwl/viewer/domain/ROBundle.java …ewer/domain/researchobject/ROBundle.javasrc/main/java/org/commonwl/viewer/domain/ROBundle.java renamed to src/main/java/org/commonwl/viewer/domain/researchobject/ROBundle.java src/main/java/org/commonwl/viewer/domain/ROBundle.java renamed to src/main/java/org/commonwl/viewer/domain/researchobject/ROBundle.java

@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain;
+package org.commonwl.viewer.domain.researchobject;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
@@ -26,6 +26,7 @@
 import org.apache.taverna.robundle.manifest.Agent;
 import org.apache.taverna.robundle.manifest.Manifest;
 import org.apache.taverna.robundle.manifest.PathMetadata;
+import org.commonwl.viewer.domain.GithubDetails;
 import org.commonwl.viewer.services.GitHubService;
 import org.eclipse.egit.github.core.RepositoryContents;
 import org.slf4j.Logger;

src/main/java/org/commonwl/viewer/services/DotWriter.java

@@ -19,9 +19,9 @@
 
 package org.commonwl.viewer.services;
 
-import org.commonwl.viewer.domain.CWLElement;
-import org.commonwl.viewer.domain.CWLStep;
 import org.commonwl.viewer.domain.Workflow;
+import org.commonwl.viewer.domain.cwl.CWLElement;
+import org.commonwl.viewer.domain.cwl.CWLStep;
 
 import java.io.IOException;
 import java.io.Writer;

src/main/java/org/commonwl/viewer/services/GitHubService.java

@@ -21,7 +21,7 @@
 
 import org.apache.commons.io.IOUtils;
 import org.commonwl.viewer.domain.GithubDetails;
-import org.commonwl.viewer.domain.HashableAgent;
+import org.commonwl.viewer.domain.researchobject.HashableAgent;
 import org.eclipse.egit.github.core.*;
 import org.eclipse.egit.github.core.client.GitHubClient;
 import org.eclipse.egit.github.core.service.CommitService;